Announcement: Prediction of Mucin type O-glycosylation sites, NetOglyc version 2.0

Jan Hansen janhan at cbs.dtu.dk
Fri May 16 07:07:10 EST 1997


Prediction of Mucin type O-glycosylation sites, NetOglyc version 2.0:

NetOglyc is a neural network algorithm recognizing Mucin type 
O-glycosylation sites in mammalian proteins.

The method have been updated with increased performance.

The method is available at:
http://www.cbs.dtu.dk/services/NetOGlyc/

both as a mail and www server.

The in vivo glycosylations sites used for making the method is
listed in O-GLYCBASE available at:
http://www.cbs.dtu.dk/databases/OGLYCBASE/

Abstract:

The specificities of the UDP-GalNAc:polypeptide
N-acetylgalactosaminyltransferase family which links the carbohydrate
GalNAc to the side chain of certain  serine and threonine residues in
mucin type glycoproteins are presently unknown. The specificity seems
to be modulated by sequence context,  secondary structure and surface
accessibility.  The  sequence context  of glycosylated threonines was
found to  differ from  that of serine, and  the sites  were  found to
cluster.  Non-clustered  sites had a sequence context different  from 
that  of  clustered  sites.  Charged  residues  were  disfavoured  at 
position -1 and +3.  A jury of artificial neural networks was trained 
to recognize  the sequence context  and surface  accessibility of 299 
known and verified mucin type  O-glycosylation sites  extracted  from 
O-GLYCBASE. The  cross-validated NetOglyc  network  system  correctly 
found  83 % of  the  glycosylated  and  90 %  of the non-glycosylated 
serine and threonine residues in independent test sets,  thus proving 
more accurate than matrix statistics and vector projection methods.

-- 
Jan Hansen

Center for Biological Sequence Analysis
Department of Physical Chemistry
The Technical University of Denmark
Building 206
DK-2800 Lyngby
Denmark

Phone:  +45 4525 2485 
Fax:    +45 4593 4808
E-mail: janhan at cbs.dtu.dk
WWW:    http://www.cbs.dtu.dk/janhan/homepage.html



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